Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites Export

@article{citeulike:4033090, abstract = {We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions of a second and third species. If multiple species have this potential TFBS in homologous positions, this program recognizes the identified TFBS as an evolutionary conserved motif (ECM). This program outputs a list of ECMs, which can be uploaded as a Custom Track in the UCSC genome browser and can be visualized along with other available data. The feasibility of this approach was tested by searching the genomes of three mammals (human, mouse and cow) with the DNA-binding motifs of YY1 and CTCF. This program successfully identified many clustered YY1- and CTCF-binding sites that are conserved among these species but were previously undetected. In particular, this program identified CTCF-binding sites that are located close to the Dlk1, Magel2 and Cdkn1c imprinted genes. Individual ChIP experiments confirmed the in vivo binding of the YY1 and CTCF proteins to most of these newly discovered binding sites, demonstrating the feasibility and usefulness of ECMFinder. 10.1093/nar/gkp077}, author = {Kang, Keunsoo and Chung, Jae H. and Kim, Joomyeong}, booktitle = {Nucl. Acids Res.}, citeulike-article-id = {4033090}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp077}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/6/2003}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19208640}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19208640}, day = {1}, doi = {10.1093/nar/gkp077}, journal = {Nucl. Acids Res.}, keywords = {conserved, discovery, motif}, month = {April}, number = {6}, pages = {2003--2013}, posted-at = {2009-02-11 09:49:19}, priority = {2}, title = {Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites}, url = {http://dx.doi.org/10.1093/nar/gkp077}, volume = {37}, year = {2009} }

TY - JOUR ID - citeulike:4033090 L3 - citeulike-article-id:4033090 N2 - We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions of a second and third species. If multiple species have this potential TFBS in homologous positions, this program recognizes the identified TFBS as an evolutionary conserved motif (ECM). This program outputs a list of ECMs, which can be uploaded as a Custom Track in the UCSC genome browser and can be visualized along with other available data. The feasibility of this approach was tested by searching the genomes of three mammals (human, mouse and cow) with the DNA-binding motifs of YY1 and CTCF. This program successfully identified many clustered YY1- and CTCF-binding sites that are conserved among these species but were previously undetected. In particular, this program identified CTCF-binding sites that are located close to the Dlk1, Magel2 and Cdkn1c imprinted genes. Individual ChIP experiments confirmed the in vivo binding of the YY1 and CTCF proteins to most of these newly discovered binding sites, demonstrating the feasibility and usefulness of ECMFinder. 10.1093/nar/gkp077 IS - 6 JF - Nucl. Acids Res. EP - 2013 TI - Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites VL - 37 T2 - Nucl. Acids Res. SP - 2003 KW - conserved KW - discovery KW - motif AU - Kang, Keunsoo AU - Chung, Jae AU - Kim, Joomyeong PY - 2009/04/01/ UR - http://dx.doi.org/10.1093/nar/gkp077 ER -